Merge pull request #511 from ngeorges-cnrs/java21_warnings

Fix build warnings

vip-api/src/main/java/fr/insalyon/creatis/vip/api/SpringWebConfig.java

@@ -63,15 +63,6 @@ public SpringWebConfig(Environment env, VipConfigurer vipConfigurer) {
         this.vipConfigurer = vipConfigurer;
     }
 
-    @Override
-    public void configurePathMatch(PathMatchConfigurer configurer) {
-        // Otherwise all that follow a dot in an URL is considered an extension and removed
-        // It's a problem for URL like "/pipelines/gate/3.2
-        // The below will become the default values in Spring 5.3
-        // Safe to use in 5.2 as long as disabling pattern match
-        configurer.setUseSuffixPatternMatch(false);
-    }
-
     @Override
     public void configureContentNegotiation(ContentNegotiationConfigurer configurer) {
         // necessary in the content negotiation stuff of carmin data

vip-api/src/main/java/fr/insalyon/creatis/vip/api/business/DataApiBusiness.java

@@ -52,6 +52,7 @@
 import fr.insalyon.creatis.vip.datamanager.server.business.TransferPoolBusiness;
 import org.apache.commons.io.FilenameUtils;
 import org.apache.commons.io.input.ReaderInputStream;
+import org.apache.commons.io.input.ReaderInputStream.Builder;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -391,8 +392,12 @@ private boolean isOperationOver(String operationId, User user)
     private void writeFileFromBase64(String base64Content, String localFilePath) throws ApiException {
         Base64.Decoder decoder = Base64.getDecoder();
         StringReader stringReader = new StringReader(base64Content);
-        InputStream inputStream = new ReaderInputStream(stringReader, StandardCharsets.UTF_8);
-        try (InputStream base64InputStream = decoder.wrap(inputStream)) {
+        try {
+            InputStream inputStream = ReaderInputStream.builder()
+                    .setReader(new StringReader(base64Content))
+                    .setCharset(StandardCharsets.UTF_8)
+                    .get();
+            InputStream base64InputStream = decoder.wrap(inputStream);
             Files.copy(base64InputStream, Paths.get(localFilePath));
         } catch (IOException e) {
             logger.error("Error writing base64 file in {}", localFilePath, e);

vip-api/src/main/java/fr/insalyon/creatis/vip/api/security/oidc/OidcResolver.java

@@ -73,6 +73,7 @@ private User getVipUser(Jwt jwt) throws BadCredentialsException {
 
     // Create authorities list from jwt claims.
     // Parsing realm_access.roles or resource_access.<resourceName>.roles is Keycloak-specific.
+    @SuppressWarnings("unchecked")
     private List<GrantedAuthority> parseAuthorities(User user, Jwt jwt) {
         List<String> roles = new ArrayList<>(); // default to no roles
         // At this point, jwt has already been verified by Spring resource server, so we assume the issuer is known (server != null).

vip-api/src/test/java/fr/insalyon/creatis/vip/api/data/AuthenticationInfoTestUtils.java

@@ -51,6 +51,7 @@ public class AuthenticationInfoTestUtils {
         authenticationInfoSuppliers = getAuthenticationInfoSuppliers();
     }
 
+    @SuppressWarnings("unchecked")
     public static Map<String, Function> getAuthenticationInfoSuppliers() {
         return JsonCustomObjectMatcher.formatSuppliers(
                 Arrays.asList("httpHeader", "httpHeaderValue"),

vip-api/src/test/java/fr/insalyon/creatis/vip/api/data/ErrorCodeAndMessageTestUtils.java

@@ -53,6 +53,7 @@ public class ErrorCodeAndMessageTestUtils {
         errorCodeAndMessageSuppliers = getErrorCodeAndMessageSuppliers();
     }
 
+    @SuppressWarnings("unchecked")
     public static Map<String,Function> getErrorCodeAndMessageSuppliers() {
         return JsonCustomObjectMatcher.formatSuppliers(
                 Arrays.asList("errorCode", "errorMessage"),

vip-api/src/test/java/fr/insalyon/creatis/vip/api/data/ExecutionTestUtils.java

@@ -158,6 +158,7 @@ public static Simulation copySimulationWithNewName(Simulation simu, String newNa
         return newSimulation;
     }
 
+    @SuppressWarnings("unchecked")
     public static Map<String,Function> getExecutionSuppliers() {
         return JsonCustomObjectMatcher.formatSuppliers(
                 Arrays.asList(

vip-api/src/test/java/fr/insalyon/creatis/vip/api/data/PathTestUtils.java

@@ -178,6 +178,8 @@ public static PathProperties getPath(Data data, boolean isDirectory,
         return pathProperties;
     }
 
+    // [WARNING] VIP-portal/vip-api/src/test/java/fr/insalyon/creatis/vip/api/data/PathTestUtils.java:[182,55] unchecked generic array creation for varargs parameter of type java.util.function.Function<fr.insalyon.creatis.vip.api.model.PathProperties,?>[]
+    @SuppressWarnings("unchecked")
     private static Map<String, Function> getPathSuppliers() {
         return JsonCustomObjectMatcher.formatSuppliers(
                 Arrays.asList("path", "lastModificationDate", "isDirectory", "exists",

vip-api/src/test/java/fr/insalyon/creatis/vip/api/data/PipelineTestUtils.java

@@ -49,6 +49,7 @@
 /**
  * Created by abonnet on 8/3/16.
  */
+@SuppressWarnings("unchecked")
 public class PipelineTestUtils {
 
     public static final Map<String,Function> pipelineSuppliers;

vip-api/src/test/java/fr/insalyon/creatis/vip/api/rest/itest/processing/ExecutionControllerIT.java

@@ -84,11 +84,12 @@ public void setUp() throws Exception {
     }
 
     @Test
+    @SuppressWarnings("unchecked")
     public void shouldListExecutions() throws Exception {
-        when(workflowDAO.get(eq(simulation1.getID()))).thenReturn(w1, null);
-        when(workflowDAO.get(eq(simulation2.getID()))).thenReturn(w2, null);
+        when(workflowDAO.get(eq(simulation1.getID()))).thenReturn(w1, (Workflow) null);
+        when(workflowDAO.get(eq(simulation2.getID()))).thenReturn(w2, (Workflow) null);
         when(workflowDAO.get(Collections.singletonList(baseUser1.getFullName()), null, null, null, null, null, null))
-                .thenReturn(Arrays.asList(w1, w2), null);
+                .thenReturn(Arrays.asList(w1, w2), (List<Workflow>) null);
 
         // perform a getWorkflows()
         mockMvc.perform(
@@ -106,9 +107,10 @@ public void shouldListExecutions() throws Exception {
     }
 
     @Test
+    @SuppressWarnings("unchecked")
     public void shouldCountExecutions() throws Exception {
         when(workflowDAO.get(Collections.singletonList(baseUser1.getFullName()), null, null, null, null, null, null))
-                .thenReturn(Arrays.asList(w1, w2), null);
+                .thenReturn(Arrays.asList(w1, w2), (List<Workflow>) null);
 
         // perform a getWorkflows()
         mockMvc.perform(
@@ -315,12 +317,13 @@ public void testPlayExecutionIsNotImplemented() throws Exception {
     }
 
     @Test
+    @SuppressWarnings("unchecked")
     public void shouldGetExecution2Results() throws Exception {
         String resultPath = "/root/user/user1/path/to/result.res";
 
-        when(workflowDAO.get(eq(simulation2.getID()))).thenReturn(w2, null);
+        when(workflowDAO.get(eq(simulation2.getID()))).thenReturn(w2, (Workflow) null);
         Output output = new Output(new OutputID("workflowID", resultPath, "processor"), DataType.URI, "port");
-        when(outputDAO.get(eq(simulation2.getID()))).thenReturn(Arrays.asList(output), null);
+        when(outputDAO.get(eq(simulation2.getID()))).thenReturn(Arrays.asList(output), (List<Output>) null);
 
         Mockito.when(server.getDataManagerUsersHome()).thenReturn("/root/user");
         Mockito.when(gridaClient.exist(resultPath)).thenReturn(true);
@@ -351,6 +354,7 @@ public void shouldKillExecution2() throws Exception
     }
 
     @Test
+    @SuppressWarnings("unchecked")
     public void testInitGwendiaExecution() throws Exception
     {
         String appName = "test application", groupName = "testGroup", className = "testClass", versionName = "4.2";
@@ -421,6 +425,7 @@ public void testInitGwendiaExecution() throws Exception
 
     // the difference (at the moment) is that with moteurLite the optional and absent parameters are not included
     @Test
+    @SuppressWarnings("unchecked")
     public void testInitBoutiquesExecution() throws Exception
     {
         String appName = "test application", groupName = "testGroup", className = "testClass", versionName = "4.2";

vip-api/src/test/java/fr/insalyon/creatis/vip/api/tools/spring/JsonCustomObjectMatcher.java

@@ -65,6 +65,7 @@ public JsonCustomObjectMatcher(T expectedBean,
         this(expectedBean, suppliers, new HashMap<>());
     }
 
+    @SuppressWarnings("unchecked")
     public JsonCustomObjectMatcher(T expectedBean,
                                    Map<String, Function> suppliers,
                                    Map<Class,Map<String,Function>> suppliersRegistry) {
@@ -88,6 +89,7 @@ public JsonCustomObjectMatcher(T expectedBean,
         nonNullPropertiesCountMatcher = equalTo(propertyMatchers.size());
     }
 
+    @SuppressWarnings("unchecked")
     private static Matcher<?> getGenericMatcher(
             Object expectedValue,
             Map<Class, Map<String, Function>> suppliersRegistry) {
@@ -133,6 +135,7 @@ private static Matcher<?> getGenericMatcher(
         }
     }
 
+    @SuppressWarnings("unchecked")
     private static Matcher<Map<String, ?>> getCustomObjectMatcherFromRegistry(
             Object o,
             Map<Class, Map<String, Function>> suppliersRegistry) {
@@ -157,6 +160,7 @@ public static <T> Matcher<Map<String,?>> jsonCorrespondsTo(
         return new JsonCustomObjectMatcher<T>(expectedBean, suppliers, suppliersRegistry);
     }
 
+    @SuppressWarnings("unchecked")
     public static <T> Map<String, Function> formatSuppliers(
             List<String> mapKeys, Function<T,?>... suppliers) {
         if (mapKeys.size() != suppliers.length) {
@@ -207,6 +211,7 @@ private static class JsonMapMatcher extends TypeSafeDiagnosingMatcher<Map<String
         private final Matcher<Integer> sizeMatcher;
         private final List<Matcher<?>> mapEntriesMatchers = new ArrayList<>();
 
+        @SuppressWarnings("unchecked")
         private JsonMapMatcher(
                 Map<?, ?> expectedMap,
                 Map<Class, Map<String, Function>> suppliersRegistry) {

vip-application/src/main/java/fr/insalyon/creatis/vip/application/client/view/monitor/ChartsTab.java

@@ -123,7 +123,7 @@ private void configureForm() {
         chartsItem.addChangedHandler(new ChangedHandler() {
             @Override
             public void onChanged(ChangedEvent event) {
-                int value = new Integer(chartsItem.getValueAsString());
+                int value = Integer.parseInt(chartsItem.getValueAsString());
                 if (value == 1 || value == 2 || value == 6) {
                     binItem.setDisabled(true);
                 } else {

vip-application/src/main/java/fr/insalyon/creatis/vip/application/client/view/monitor/StatsTab.java

@@ -123,13 +123,6 @@ private void configureForm() {
         chartsItem.setWidth(250);
         chartsItem.setValueMap(chartsMap);
         chartsItem.setEmptyDisplayValue("Select a chart...");
-        chartsItem.addChangedHandler(new ChangedHandler() {
-
-            @Override
-            public void onChanged(ChangedEvent event) {
-                int value = new Integer(chartsItem.getValueAsString());
-            }
-        });
 
         generateButton = WidgetUtil.getIButton("Get Stats", null, new ClickHandler() {
 

vip-application/src/main/java/fr/insalyon/creatis/vip/application/client/view/monitor/chart/GeneralBarChart.java

@@ -135,7 +135,7 @@ public void build(String caption, String color, int binSize) {
                             max = localMax;
                         }
                         if (res.length > 4) {
-                            sum += new Integer(res[4]);
+                            sum += Integer.parseInt(res[4]);
                         }
                     }
                 }

vip-application/src/main/java/fr/insalyon/creatis/vip/application/server/business/ReproVipBusiness.java

@@ -316,6 +316,7 @@ private Map<String, String> mapOutputDataPathsByFilenames(List<String> outputDat
         return outputDataMap;
     }
 
+    @SuppressWarnings("unchecked")
     private Map<String, String> getOutputFilenamesFromProvenanceFile(Path provenanceFilePath) throws BusinessException {
         try {
             Map<?, ?> map = new ObjectMapper().readValue(provenanceFilePath.toFile(), Map.class);

vip-application/src/main/java/fr/insalyon/creatis/vip/application/server/business/WorkflowBusiness.java

@@ -68,6 +68,7 @@
 import org.springframework.transaction.annotation.Transactional;
 import org.xml.sax.SAXException;
 
+import javax.xml.parsers.ParserConfigurationException;
 import java.io.File;
 import java.io.IOException;
 import java.util.*;
@@ -390,7 +391,7 @@ public Descriptor getApplicationDescriptor(
             }
             return getGwendiaParser().parse(workflowPath);
 
-        } catch (SAXException | IOException ex) {
+        } catch (SAXException | ParserConfigurationException | IOException ex) {
             logger.error("Error getting application descriptor for {}/{}", applicationName, applicationVersion, ex);
             throw new BusinessException(WRONG_APPLICATION_DESCRIPTOR, ex, applicationName + "/" + applicationVersion);
         } catch (DAOException | BusinessException ex) {

vip-application/src/main/java/fr/insalyon/creatis/vip/application/server/business/simulation/parser/AbstractWorkflowParser.java

@@ -39,6 +39,8 @@
 import org.xml.sax.helpers.DefaultHandler;
 import org.xml.sax.helpers.XMLReaderFactory;
 
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.parsers.SAXParserFactory;
 import java.io.FileReader;
 import java.io.IOException;
 import java.io.Reader;
@@ -61,16 +63,18 @@ protected AbstractWorkflowParser() {
         sources = new ArrayList<Source>();
     }
 
-    public Descriptor parse(String fileName) throws IOException, SAXException {
+    public Descriptor parse(String fileName) throws IOException, SAXException, ParserConfigurationException {
         return parse(new FileReader(fileName));
     }
 
-    public Descriptor parseString(String workflowString) throws IOException, SAXException {
+    public Descriptor parseString(String workflowString) throws IOException, SAXException, ParserConfigurationException {
         return parse(new StringReader(workflowString));
     }
 
-    private Descriptor parse(Reader workflowReader) throws IOException, SAXException {
-        reader = XMLReaderFactory.createXMLReader();
+    private Descriptor parse(Reader workflowReader) throws IOException, SAXException, ParserConfigurationException {
+        SAXParserFactory parserFactory = SAXParserFactory.newInstance();
+        parserFactory.setNamespaceAware(true);
+        reader = parserFactory.newSAXParser().getXMLReader();
         reader.setContentHandler(this);
         reader.parse(new InputSource(workflowReader));
 

vip-application/src/main/java/fr/insalyon/creatis/vip/application/server/business/simulation/parser/InputM2Parser.java

@@ -56,6 +56,9 @@
 import org.xml.sax.helpers.DefaultHandler;
 import org.xml.sax.helpers.XMLReaderFactory;
 
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.parsers.SAXParserFactory;
+
 /**
  * Parse a m2 input file.
  *
@@ -93,13 +96,15 @@ public Map<String, String> parse(String fileName)
             throws BusinessException {
 
         try {
-            XMLReader reader = XMLReaderFactory.createXMLReader();
+            SAXParserFactory parserFactory = SAXParserFactory.newInstance();
+            parserFactory.setNamespaceAware(true);
+            XMLReader reader = parserFactory.newSAXParser().getXMLReader();
             reader.setContentHandler(this);
             reader.parse(new InputSource(new FileReader(fileName)));
 
             return inputs;
 
-        } catch (IOException | SAXException ex) {
+        } catch (IOException | SAXException | ParserConfigurationException ex) {
             logger.error("Error parsing {}", fileName, ex);
             throw new BusinessException(ex);
         }

vip-application/src/main/java/fr/insalyon/creatis/vip/application/server/business/simulation/parser/InputParser.java

@@ -45,6 +45,9 @@
 import org.xml.sax.helpers.DefaultHandler;
 import org.xml.sax.helpers.XMLReaderFactory;
 
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.parsers.SAXParserFactory;
+
 /**
  * Parse a input file.
  *
@@ -69,13 +72,15 @@ public InputParser() {
 
     public String parse(String fileName) throws BusinessException {
         try {
-            reader = XMLReaderFactory.createXMLReader();
+            SAXParserFactory parserFactory = SAXParserFactory.newInstance();
+            parserFactory.setNamespaceAware(true);
+            reader = parserFactory.newSAXParser().getXMLReader();
             reader.setContentHandler(this);
             reader.parse(new InputSource(new FileReader(fileName)));
 
             return inputs.toString();
 
-        } catch (IOException | SAXException ex) {
+        } catch (IOException | SAXException | ParserConfigurationException ex) {
             logger.error("Error parsing file {}", fileName, ex);
             throw new BusinessException(ex);
         }

vip-application/src/main/java/fr/insalyon/creatis/vip/application/server/rpc/WorkflowServiceImpl.java

@@ -52,6 +52,7 @@
 import org.slf4j.LoggerFactory;
 
 import jakarta.servlet.ServletException;
+
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.FileReader;

vip-application/src/main/java/localhost/moteur_service_wsdl/Moteur_ServiceLocator.java

@@ -31,6 +31,8 @@
  */
 package localhost.moteur_service_wsdl;
 
+import java.net.URISyntaxException;
+
 public class Moteur_ServiceLocator extends org.apache.axis.client.Service implements localhost.moteur_service_wsdl.Moteur_Service {
 
     /**
@@ -71,9 +73,11 @@ public void setmoteur_serviceWSDDServiceName(java.lang.String name) {
     public localhost.moteur_service_wsdl.Moteur_servicePortType getmoteur_service() throws javax.xml.rpc.ServiceException {
         java.net.URL endpoint;
         try {
-            endpoint = new java.net.URL(moteur_service_address);
+            endpoint = new java.net.URI(moteur_service_address).toURL();
         } catch (java.net.MalformedURLException e) {
             throw new javax.xml.rpc.ServiceException(e);
+        } catch (URISyntaxException e) {
+            throw new javax.xml.rpc.ServiceException(e);
         }
         return getmoteur_service(endpoint);
     }
@@ -100,7 +104,7 @@ public void setmoteur_serviceEndpointAddress(java.lang.String address) {
     public java.rmi.Remote getPort(Class serviceEndpointInterface) throws javax.xml.rpc.ServiceException {
         try {
             if (localhost.moteur_service_wsdl.Moteur_servicePortType.class.isAssignableFrom(serviceEndpointInterface)) {
-                localhost.moteur_service_wsdl.Moteur_BindingStub _stub = new localhost.moteur_service_wsdl.Moteur_BindingStub(new java.net.URL(moteur_service_address), this);
+                localhost.moteur_service_wsdl.Moteur_BindingStub _stub = new localhost.moteur_service_wsdl.Moteur_BindingStub(new java.net.URI(moteur_service_address).toURL(), this);
                 _stub.setPortName(getmoteur_serviceWSDDServiceName());
                 return _stub;
             }

vip-application/src/test/java/fr/insalyon/creatis/vip/application/integrationtest/PublicApplicationListIT.java

@@ -34,8 +34,8 @@ public void shouldNotIncludePrivateGroupsAndClasses() throws BusinessException,
         Group privateGroup = new Group("private group", false, true, true);
         // classes are not really public/private, but they are linked to public/private groups
         // a class is considered private if it is linked only to private groups
-        AppClass publicClass = new AppClass("public class", Collections.EMPTY_LIST, Collections.singletonList(publicGroup.getName()));
-        AppClass privateClass = new AppClass("private class", Collections.EMPTY_LIST, Collections.singletonList(privateGroup.getName()));
+        AppClass publicClass = new AppClass("public class", Collections.emptyList(), Collections.singletonList(publicGroup.getName()));
+        AppClass privateClass = new AppClass("private class", Collections.emptyList(), Collections.singletonList(privateGroup.getName()));
         Application app = new Application("testApp", Arrays.asList(publicClass.getName(), privateClass.getName()), "");
         AppVersion appVersion = new AppVersion(app.getName(), "", null, null, true, false);
         // persist data in database

vip-core/src/main/java/fr/insalyon/creatis/vip/core/server/auth/SamlAuthenticationService.java

@@ -37,6 +37,7 @@
 import java.io.IOException;
 import java.io.UnsupportedEncodingException;
 import java.net.MalformedURLException;
+import java.net.URISyntaxException;
 import java.security.NoSuchAlgorithmException;
 import java.security.cert.CertificateException;
 import java.security.spec.InvalidKeySpecException;
@@ -139,7 +140,7 @@ protected void checkValidRequest(HttpServletRequest request) throws BusinessExce
                 logger.error("Error with SAML assertion {} : audience is not valid", new String(xmlAssertion));
                 throw new BusinessException("Assertion audience is not valid!");
             }
-        } catch (MalformedURLException ex) {
+        } catch (MalformedURLException | URISyntaxException ex) {
             logger.error("Error with SAML assertion {}", new String(xmlAssertion), ex);
             throw new BusinessException(ex);
         }